Distribution and characterization of simple sequence repeats in Gossypium raimondii genome

Simple sequence repeats (SSRs) can be derived from the complete genome sequence. These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop SSRs for cotton gene mapping, we selected the complete genome sequence of Gossypium raimondii, which consisted of 4447 non-redundant scaffolds. Out of 775.2 Mb sequence examined, a total of 136,345 microsatellites were identified with a density of 5.69 kb per SSR in the G. raimondii genome leading to development of 112,177 primer pairs. The distributions of SSRs in the genome were non-random. Among the different motifs ranging from 1 to 6 bp, penta-nucleotide repeats were most abundant (30.5%), followed by tetra-nucleotide repeats (18.2%) and di-nucleotide repeats (16.9%). Among all identified 457 motif types, the most frequently occurring repeat motifs were poly-AT/TA, which accounted for 79.8% of the total di-nt SSRs, followed by AAAT/TTTA with 51.5% of the total tetra-nucleotede. Further, 18,834 microsatellites were detected from the protein-coding genes, and the frequency of gene containing SSRs was 46.0% in 40,976 genes of G. raimondii. These genome-based SSRs developed in the present study will lay the groundwork for developing large numbers of SSR markers for genetic mapping, gene discovery, genetic diversity analysis, and MAS breeding in cotton.     

基于比较基因组学的高地芽孢杆菌6ww6分子标识筛选及其快速鉴定

【目的】高地芽孢杆菌(Bacillus altitudinis) 6ww6是一株根际耐盐促生菌,可以作为微生物肥料的优选菌种。为了加强菌种知识产权保护,建立菌株快速检测方法。【方法】本研究通过基因组比对分析、TBLASTn检索、NR库检索验证并剔除有其他同源的结果序列,最终得到菌株6ww6的孤儿基因,设计引物进行PCR鉴定。【结果】筛选出5个特异性基因J939_13195、J9319_05960、J9319_13355、J9319_05965和J9319_13350。引物5960F和5960R可以单一性扩增出菌株6ww6的目的基因J9319_05960,确定其为菌株6ww6的特异性分子标识。【结论】本研究确定了菌株6ww6的唯一性身份编码,建立了以比较基因组学和孤儿基因为基础的菌株水平上的鉴定方法。该方法具有快速、精确、能鉴定到菌株水平的优点,对于有价值微生物的知识产权保护提供了有力的抓手。     

家燕营巢特征及其对城市环境的适应性

城市面积在全球范围内迅速扩张,一些鸟类种群通过改变营巢特征,在与自然生境截然不同的城市中筑巢繁殖。但目前城市环境对于鸟类营巢影响的研究较缺乏。为了解鸟类营巢对城市环境的适应,于2016、2019年在黑龙江哈尔滨的城市与乡村环境,分别测量家燕（Hirundo rustica）巢（如,大小及形状）及巢址特征等（如,距地面和屋顶距离）参数,以探究：（1）家燕巢特征在乡村及城市生境是否存在差异？（2）家燕巢特征在年际间是否存在变化？并为城市家燕种群的保护提供理论依据及合理建议。研究采用Kruskal-Wallis秩和检验以及Wilcoxon秩和检验比较分析所测量的巢特征参数在城乡之间、年际间的差异,并对组间参数进行线性判别分析（LDA,Linear Discriminant Analysis）。结果发现,城乡间具有显著差异：（1）与乡村相比,城市巢距离屋顶更远,距地相对更近（P<0.05）;（2）城市巢更浅（P<0.05）;（3）从2016到2019年,城市和乡村巢都变得更深,半径更大（P<0.05）。根据这些发现,推测城市楼房建筑的楼道为家燕繁殖提供了相对更为封闭、安全的环境,旧巢及较为丰富的支撑物为家燕提供了适宜的巢址,有可能节省亲鸟在营巢上的繁殖投入;但同时应当警惕门窗关闭、资源受限、人为干扰等不利因素可能造成的生态陷阱。     

Can eggs in a cavity be a female secondary sexual signal? Male nest visits and modelling of egg visual discrimination in blue tits

Eggshell colouration is thought to function as a female-specific secondary sexual trait. While tests of this idea are rapidly accumulating in cavity-nesting birds, some fundamental underlying assumptions remain rarely investigated: namely, can males see eggshell coloration and perceive colour differences between the eggs of different females? We tested these two key assumptions in a natural population of blue tits (Cyanistes caeruleus). Using transponders, we tracked male nest visits and found that all males visited their nest-boxes while eggs were present and often visually accessible. Interestingly, some males also visited neighbouring nests. We then tested whether birds could detect eggshell coloration using models of avian colour vision; models were performed with and without limitations on visual performance owing to dim light. Both models found that differences in eggshell brightness were often easier to discriminate than differences in colour; there was more contrast in white eggshell background between clutches than within and its contrast against nest background was repeatable within clutches, suggesting these features could act as signals. Yet, the detectability of these contrasts depended entirely on model assumptions of visual limitations. Consequently, we need a better understanding of underlying visual mechanisms in dim-light environments and behavioural discrimination experiments before confirming the signalling potential of eggshell coloration.     

药用野生稻转育后代一个抗白叶枯病新基因的定位

从药用野生稻渗入后代选育的水稻株系B5表现为高抗褐飞虱、白背飞虱和白叶枯病。对B5与籼稻品种明恢63杂交组合的187个重组自交系(RILs)进行了抗白叶枯病接种鉴定,采用分离集团分析法(Bulked Segregant Analysis,BSA),在第1染色体上筛选到与水稻抗白叶枯病基因相连锁RFLP分子标记。利用RILs抗病性表现型鉴定资料和构建的分子标记连锁图谱,将抗白叶枯病基因定位在第1染色体短臂的C904和R596之间,这两个分子标记间遗传距离为1．3cM。该基因对RILs群体抗病性变异的贡献率为52．96％,是一效应值较大的主效基因。这一抗白叶枯病基因不同于已报道的抗白叶枯病基因的位点,因此将其命名为Xa29(t)。     

A hierarchical nest survival model integrating incomplete temporally varying covariates

Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood‐feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the biting‐insect hypothesis and other hypotheses for nesting failure in this reintroduced population; resulting inferences will support ongoing efforts to manage this population via an adaptive management approach. Wider application of our approach offers promise for modeling the effects of other temporally varying, but imperfectly observed covariates on nest survival, including the possibility of modeling temporally varying covariates collected from incubating adults.     

遗传标记和免疫学方法在实验动物质量控制中的应用

生命科学发展迅速,实验动物级别逐渐提高,在保证生物制品实验结果可靠性前提下,完善动物由低级别向高级别过渡显得十分必要,最终目的达到实验动物标准化和动物实验规范化。对实验动物质量控制中的遗传标记和免疫学方法进行了综述。     

First record of colour polymorphism in the Neotropical apple snail Asolene platae: inheritance mechanism and evidence for multiple paternity

Asolene platae (Ampullariidae) is a dioecious freshwater snail with subaquatic gelatinous egg masses that dwells in the Río de la Plata basin (Argentina). The aim of this study was to describe the inheritance mechanism of the colour variations of the shell and soft parts of this snail, and to study their potential use as a genetic marker. The wild-type phenotype presents dark pigments in the soft parts and in shell bands, whereas the yellow phenotype lacks dark pigments in the soft parts and also most dark bands in the shell, except for a subsutural and a periumbilical band. The data showed that the lack of pigments in A. platae is a recessive homozygotic condition with a simple Mendelian inheritance mechanism. Females of the wild-type phenotype had a higher number of bands than the males. The pigment of the bands of both phenotypes is located in the calcareous matrix of the shell. Using the lack of pigments as a genetic marker we demonstrated the existence of biparental egg masses in A. platae, hitherto known in only one species within the Ampullariidae.     

QTL复合区间作图中标记筛选的效率及其影响因素研究

高效地筛选标记 ,是复合区间作图方法定位QTLs的基础。筛选出的主效标记和互作标记 ,除了用作控制背景遗传效应外 ,在定位具有上位性效应的QTLs时 ,还将用于构筑两维搜索区间。因而 ,标记筛选的效率将直接影响QTL定位的功效和精度。通过对不同方法筛选标记的效率进行模拟研究 ,发现回归方法明显优于随机效应预测方法 ,同归方法中又以前向选择法简单有效。普通遗传力和基因型×环境互作遗传力的增加都能提高标记筛选效率 ,前者对主效应较大的QTLs影响明显 ,后者对主效应较小的QTLs作用较大。过多过密的标记会降低标记筛选效率 ,其中密度增加对标记筛选的负作用更为突出。为了缓解标记筛选效率制约QTL定位功效的缺陷 ,可以用多环境下筛选出的标记共同构建两维搜索区间     

无环鸟苷抗乙型肝炎病毒复制长短程疗法随访观察

慢性乙型肝炎病毒感染s5例,随机分无环鸟苷长程组22例,短程组11例和对照组22例。经一年随访观察,无环鸟苷治疗组见血清HBeAg、DNA-P和HBV-DNA有规律性阴转,短程组于12个月又有部分指标阳转,长程组阴转较多,其血清HBeAg、DNA-P和HBV-DNA阴转率与短程和对照组比较有显著性差异。一年结果四项病毒复制指标全部阴转例数与对照组有显著性差异,结果表明,无环鸟苷长疗程是有较好疗效。